Using MS Cleaner (Web-Version)

User interface flags	Description
input file	This edit box displays the input data files to be cleaned. Either type in the path name of a single file, or click the browse button to select file(s) from an open file dialog box. Supported data formats are: - Sequest files (.dta), single spectra - Mascot generic files (.mgf), multiple spectra
input type	Choose .mgf, .dta or automatic detection
multi-charge deconvolution	If selected, the program detects multi-charged isotope peak clusters according to the chosen Deconvolution threshold. These are then transformed into a single monoisotopic peak. All other signals from the cluster are deleted.
deconvolution threshold	The deconvolution procedure detects multi-charged peaks if the correlation coefficient is higher than this value.
de-isotoping	If selected, the program detects singly-charged isotope peak clusters according to the chosen Deisotoping threshold. These are then transformed into a single monoisotopic peak. All other signals from the cluster are deleted.
de-isotop filter width	Specifies the deisotoping filter width.
de-isotop threshold	The deisotoping procedure reduces the intensity of the potential isotope peaks. If the decrease in intensity is greater than this threshold value, the intensity of the peak will be set to zero.
random noise removal	If selected, the program removes random noise from the spectrum according to the Random noise threshold.
random noise threshold	This filter reduces the intensity of random noise peaks. If the decrease in intensity is greater than this value, the intensity is set to zero.
check sequence tags	When this option is selected, the program inspects each MS2 spectrum for a series of peak spacing with m/z values corresponding to amino acids mass (with certain mass tolerance) - known as a sequence tag. The user can define the length of the sequence tag in the accompanying-box (values in the range 2 to 5 are recommended). The presence of a sequence tag indicates that the spectrum is likely of protein origin. Spectra without a sequence tag (likely derived from non-protein polymer contaminants) are classified as 'bad'.
sequence tags length	Specifies the length of the sequence tag.
bad spectra	Determines bad spectra handling. Selecting "leave" will leave spectra designated as "bad" in the "cleaned" output file. Using this option doesn't separate bad spectra from remaining files. Selecting the "separate" option creates two sets of output file(s): cleaned files (minus the bad spectra), and bad spectra files. Selecting the "delete" option deletes the bad spectra from the output files.
soft bad-spectra detection	Using this option, fewer bad spectra will be identified. This mode is used if a high sequence coverage is more important than data reduction.
merge peaks	If selected, the program merges together peaks that are closer than the Merge Peaks Spacing value.
merge peaks spacing/least peak spacing	Specifies the least allowed spacing between peaks for the Merge peaks algorithm of the program.
median filter	Specifies how many signals are taken for median filtering of the power spectrum.
max power spectrum periodicity/frequency	Specifies the maximum allowed frequency of the power spectrum.
band stop frequency/random noise filter	This is the stop frequency for the low pass filter used for random noise removal.
mass tolerance	Mass tolerance taken into account during the sequence tag determination.
sequence ladder intensity	Percentage of the top of the intensity ranked peaks among which the sequence ladder is searched for.